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Adds a phyx2ontology.js script for building a synthesized Clade Ontology #58

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merged 38 commits into from
Mar 27, 2019
Merged

Adds a phyx2ontology.js script for building a synthesized Clade Ontology #58

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37d6109
Added dependencies for phyx2ontology.js.
gaurav Feb 26, 2019
1c203ac
Added taxonomic unit matching.
gaurav Dec 6, 2018
29ea7e0
Method PhylorefWrapper.exportAsJSONLD renamed to asJSONLD.
gaurav Dec 6, 2018
0910203
Updated phyx2ontology to use @phyloref/phyx from NPM.
gaurav Feb 7, 2019
37e18bb
Annotated node with expected phyloref as per #4.
gaurav Feb 7, 2019
2275da5
Updated Phyloref Ontology used to 2018-12-14 version and included TCAN.
gaurav Feb 7, 2019
939bd0f
Include annotations for phylorefs in expectedPhyloreferenceNamed.
gaurav Feb 7, 2019
5fa19ba
Updated @phyloref/phyx to latest and updated the Phyx context URI.
gaurav Feb 8, 2019
7e2e404
Annotated phylogeny nodes with taxonomic units when scientific names.
gaurav Feb 8, 2019
6c07e0b
First stab at Model 2.0 resolution for phylorefs with 1 int/1 ext.
gaurav Feb 8, 2019
5611281
Switched terms being produced in CLADO.
gaurav Feb 8, 2019
322775f
Use ScientificNameWrapper to consistently find the binomial name.
gaurav Feb 8, 2019
4a05e77
Added support for 2 internal specifiers with no external specifiers.
gaurav Feb 8, 2019
cef3dc8
First stab at adding support for MRCA definitions.
gaurav Feb 15, 2019
43665b9
Cleaned up code a little so the roles of each function is clearer.
gaurav Feb 16, 2019
bb6086b
Cleaned up generating additional classes slightly.
gaurav Feb 16, 2019
fb93ea3
First stab at external specifiers.
gaurav Feb 18, 2019
b448a35
We now produce reasonable sensible external phylorefs.
gaurav Feb 18, 2019
d01f9c8
Make parent nodes explicit in RDF as role inverses not in OWL EL.
gaurav Feb 19, 2019
248cb68
Added basic support for specimen matching by occurrenceID/organismID.
gaurav Feb 19, 2019
b5f1315
Created simplified form for the 1 internal/1 external case.
gaurav Feb 20, 2019
0a18bb3
Cleaned up cases where we need to add a has_Ancestor check.
gaurav Feb 21, 2019
21061e4
Realized how to check whether we need the has_Ancestor check or not.
gaurav Feb 21, 2019
9efdfdd
Added eslint and used it to clean up phyx2ontology.js.
gaurav Feb 21, 2019
2fad673
Support for converting Phyx files to JSON-LD.
gaurav Feb 25, 2019
b124dbe
Made phylogeny output optional, removed TUmatches.
gaurav Feb 25, 2019
949732a
Updated phyx2ontology.js to meet the ESLint style guide.
gaurav Feb 26, 2019
123ba2a
Added an NPM 'script' to generate the ontology in JSON-LD.
gaurav Feb 27, 2019
9a9de81
Simplified specimen restriction as per phyloref/clade-ontology#61.
gaurav Feb 27, 2019
8b79c76
Started cleaning up and documenting phyx2ontology.js for review.
gaurav Feb 27, 2019
2d3ba13
Improved comments of export.
gaurav Mar 7, 2019
6d1e1f6
Moved some methods out of phyx2ontology.js into a separate file.
gaurav Mar 7, 2019
8fa6b24
Eliminated TU matching, which is no longer needed in Model 2.0.
gaurav Mar 7, 2019
82a0c81
Improved comments in phyx2ontology.js.
gaurav Mar 7, 2019
46e2eb2
Added more documentation.
gaurav Mar 8, 2019
2e340e2
Improved documentation.
gaurav Mar 9, 2019
fd69735
Removed requirement to pass in equivalent class as a function.
gaurav Mar 9, 2019
74116ad
Added a very simple test for phyx2ontology.js.
gaurav Mar 26, 2019
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